{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### This notebook plots a graph showing the indice of similariries both intra-document (comparing a document with itself) and inter-documents (comparing a document against other documents)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "#!pip install git+https://github.com/python-quantities/python-quantities.git --user"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "scrolled": false
   },
   "outputs": [
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      "/home/oreilly/curator_DB/10.1016%2F0006-8993(86)91340-5.pdf /home/oreilly/curator_DB/10.1016%2F0006-8993(86)91340-5.pdf\n",
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     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "/home/oreilly/curator_DB/10.1016%2Fj.tins.2005.04.003.pdf /home/oreilly/curator_DB/10.1016%2Fj.tins.2005.04.003.pdf\n",
      "/home/oreilly/curator_DB/10.1038%2Fnn.3488.pdf /home/oreilly/curator_DB/10.1038%2Fnn.3488.pdf\n",
      "/home/oreilly/curator_DB/10.1002%2Fcne.22350.pdf /home/oreilly/curator_DB/10.1002%2Fcne.22350.pdf\n",
      "/home/oreilly/curator_DB/10.1093%2Fcercor%2F3.5.373.pdf /home/oreilly/curator_DB/10.1093%2Fcercor%2F3.5.373.pdf\n",
      "/home/oreilly/curator_DB/10.1523%2FJNEUROSCI.4677-06.2007.pdf /home/oreilly/curator_DB/10.1523%2FJNEUROSCI.4677-06.2007.pdf\n",
      "/home/oreilly/curator_DB/10.1002%2Fcne.21671.pdf /home/oreilly/curator_DB/10.1002%2Fcne.21671.pdf\n",
      "/home/oreilly/curator_DB/10.1111%2Fj.1530-0277.2011.01557.x.pdf /home/oreilly/curator_DB/10.1111%2Fj.1530-0277.2011.01557.x.pdf\n",
      "/home/oreilly/curator_DB/10.1007%2Fs12264-013-1402-3.pdf /home/oreilly/curator_DB/10.1007%2Fs12264-013-1402-3.pdf\n",
      "/home/oreilly/curator_DB/10.1152%2Fjn.00926.2014.pdf /home/oreilly/curator_DB/10.1152%2Fjn.00926.2014.pdf\n",
      "/home/oreilly/curator_DB/10.1111%2Fj.1469-7793.2000.00571.x.pdf /home/oreilly/curator_DB/10.1111%2Fj.1469-7793.2000.00571.x.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2FS0165-3806(98)00097-2.pdf /home/oreilly/curator_DB/10.1016%2FS0165-3806(98)00097-2.pdf\n",
      "/home/oreilly/curator_DB/10.1113%2Fjphysiol.2004.070888.pdf /home/oreilly/curator_DB/10.1113%2Fjphysiol.2004.070888.pdf\n",
      "/home/oreilly/curator_DB/PMID_10407013.pdf /home/oreilly/curator_DB/PMID_10407013.pdf\n",
      "/home/oreilly/curator_DB/PMID_7711934.pdf /home/oreilly/curator_DB/PMID_7711934.pdf\n",
      "/home/oreilly/curator_DB/PMID_11218057.pdf /home/oreilly/curator_DB/PMID_11218057.pdf\n",
      "/home/oreilly/curator_DB/10.1155%2F2014%2F370764.pdf /home/oreilly/curator_DB/10.1155%2F2014%2F370764.pdf\n",
      "/home/oreilly/curator_DB/10.1155%2F2016%2F3024342.pdf /home/oreilly/curator_DB/10.1155%2F2016%2F3024342.pdf\n",
      "/home/oreilly/curator_DB/10.1523%2FJNEUROSCI.0562-14.2014.pdf /home/oreilly/curator_DB/10.1523%2FJNEUROSCI.0562-14.2014.pdf\n",
      "/home/oreilly/curator_DB/PMID_1331356.pdf /home/oreilly/curator_DB/PMID_1331356.pdf\n",
      "/home/oreilly/curator_DB/10.1111%2Fejn.12874.pdf /home/oreilly/curator_DB/10.1111%2Fejn.12874.pdf\n",
      "/home/oreilly/curator_DB/PMID_7711933.pdf /home/oreilly/curator_DB/PMID_7711933.pdf\n",
      "/home/oreilly/curator_DB/10.1152%2Fjn.91130.2008.pdf /home/oreilly/curator_DB/10.1152%2Fjn.91130.2008.pdf\n",
      "/home/oreilly/curator_DB/10.1113%2Fjphysiol.2006.113043.pdf /home/oreilly/curator_DB/10.1113%2Fjphysiol.2006.113043.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2Fj.conb.2015.02.003.pdf /home/oreilly/curator_DB/10.1016%2Fj.conb.2015.02.003.pdf\n",
      "/home/oreilly/curator_DB/PMID_9824459.pdf /home/oreilly/curator_DB/PMID_9824459.pdf\n",
      "/home/oreilly/curator_DB/10.1371%2Fjournal.pone.0107780.pdf /home/oreilly/curator_DB/10.1371%2Fjournal.pone.0107780.pdf\n",
      "/home/oreilly/curator_DB/10.1002%2Fcne.902580308.pdf /home/oreilly/curator_DB/10.1002%2Fcne.902580308.pdf\n",
      "/home/oreilly/curator_DB/10.3389%2Ffncom.2016.00079.pdf /home/oreilly/curator_DB/10.3389%2Ffncom.2016.00079.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2Fj.neuron.2009.05.015.pdf /home/oreilly/curator_DB/10.1016%2Fj.neuron.2009.05.015.pdf\n",
      "/home/oreilly/curator_DB/PMID_10391450.pdf /home/oreilly/curator_DB/PMID_10391450.pdf\n",
      "/home/oreilly/curator_DB/10.1007%2Fs11055-006-0134-5.pdf /home/oreilly/curator_DB/10.1007%2Fs11055-006-0134-5.pdf\n",
      "/home/oreilly/curator_DB/10.1152%2Fjn.00559.2012.pdf /home/oreilly/curator_DB/10.1152%2Fjn.00559.2012.pdf\n",
      "/home/oreilly/curator_DB/10.1016_j.mcn.2008.07.012.pdf /home/oreilly/curator_DB/10.1016_j.mcn.2008.07.012.pdf\n",
      "/home/oreilly/curator_DB/10.1371%2Fjournal.pbio.1000348.pdf /home/oreilly/curator_DB/10.1371%2Fjournal.pbio.1000348.pdf\n",
      "/home/oreilly/curator_DB/10.1111%2Fejn.12098.pdf /home/oreilly/curator_DB/10.1111%2Fejn.12098.pdf\n",
      "/home/oreilly/curator_DB/PMID_3559675.pdf /home/oreilly/curator_DB/PMID_3559675.pdf\n",
      "/home/oreilly/curator_DB/10.1162%2Fneco.2006.18.12.3052.pdf /home/oreilly/curator_DB/10.1162%2Fneco.2006.18.12.3052.pdf\n",
      "/home/oreilly/curator_DB/PMID_8613783.pdf /home/oreilly/curator_DB/PMID_8613783.pdf\n",
      "/home/oreilly/curator_DB/10.1152%2Fjn.01163.2002.pdf /home/oreilly/curator_DB/10.1152%2Fjn.01163.2002.pdf\n",
      "/home/oreilly/curator_DB/10.1073%2Fpnas.0402761101.pdf /home/oreilly/curator_DB/10.1073%2Fpnas.0402761101.pdf\n",
      "/home/oreilly/curator_DB/10.1002%2Fcne.901300404.pdf /home/oreilly/curator_DB/10.1002%2Fcne.901300404.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2FS0006-3495(93)81297-9.pdf /home/oreilly/curator_DB/10.1016%2FS0006-3495(93)81297-9.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2F0047-6374(96)01752-6.pdf /home/oreilly/curator_DB/10.1016%2F0047-6374(96)01752-6.pdf\n",
      "/home/oreilly/curator_DB/10.1146%2Fannurev-neuro-071013-014229.pdf /home/oreilly/curator_DB/10.1146%2Fannurev-neuro-071013-014229.pdf\n",
      "/home/oreilly/curator_DB/PMID_2833597.pdf /home/oreilly/curator_DB/PMID_2833597.pdf\n",
      "/home/oreilly/curator_DB/PMID_9115669.pdf /home/oreilly/curator_DB/PMID_9115669.pdf\n",
      "/home/oreilly/curator_DB/10.1016%2Fj.neuron.2015.03.040.pdf /home/oreilly/curator_DB/10.1016%2Fj.neuron.2015.03.040.pdf\n"
     ]
    }
   ],
   "source": [
    "import nat.restClient as client\n",
    "from importlib import reload\n",
    "\n",
    "reload(client)\n",
    "\n",
    "# A path pointing to a NeuroCurator database containing at least some PDFs.\n",
    "db_path = \"/home/oreilly/curator_DB\"\n",
    "\n",
    "# Will compute similarities. Can take a long time, depending on the number of PDF. \n",
    "intra, inter = client.checkSimilarities(db_path, sample_size=100)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Sanity check. The intra-class similarity should always be larger and the inter-class similarity. The server threshold to decide if a document submitted is the same as the one on the server is currently set at 0.6."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "0.0533791415585 0.65168356398\n"
     ]
    },
    {
     "data": {
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      "text/plain": [
       "<matplotlib.figure.Figure at 0x7f09d89186a0>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "%matplotlib inline\n",
    "import seaborn as sb\n",
    "import matplotlib.pylab as plt\n",
    "\n",
    "if len(intra):\n",
    "    print(min(intra), max(inter))\n",
    "    sb.distplot(intra, kde=False, norm_hist=True)\n",
    "    sb.distplot(inter, kde=False, norm_hist=True)\n",
    "    plt.axvline(x=0.6)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "python3.5",
   "language": "python",
   "name": "python3.5"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.5.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 1
}
